Abstract The present work focuses on the mineralogy and the reactivity of clinkers made from the integration of natural fluorapatite in the raw meals with percentages ranging from 0 up to15%. The samples were characterized by infrared spectrometry, X-ray diffraction and microscopy techniques. The distribution of phosphorous and fluorine into clinkers minerals was determined by MEB/EDS mapping. The mineralogical composition was determined by XRD/Rietveld and the samples reactivity followed by isothermal microcalorimetry. It has been found that fluorine stabilizes C3S and β-C2S which still are found with high levels of P2O5. Cements obtained from up to 8% natural fluorapatite incorporation still present acceptable properties. Natural fluorapatite could have an important potential as decarbonised source of CaO contributing to decrease the CO2 emission in cement industry.